All Questions
Tagged with phylogenetics snp
25 questions
1
vote
0
answers
65
views
SNP How to detect regions of erratic pairwise alignment?
I have clusters of DNA sequences that contain some mutations. All the sequences in a cluster should contain the same mutations.
As the mutations aren't known, those clusters of sequences were pairwise-...
- 181
2
votes
1
answer
84
views
What tool I can use to map short-reads sequences to reference genome and get specific mapped size
I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle.
Anyone knows what bioinformatics tool I can ...
- 21
1
vote
1
answer
68
views
Given SNP-Chip data for a population, what tool should I use to reconstruct haplotypes?
I think Eagle or haploSep will do the job of reconstructing haplotype data, but I'm not sure what the 'standard' or best practice tool to use is.
I have a VCF/PLINK format file of ~8,000 individuals ...
- 480
0
votes
1
answer
42
views
What to use to determine SNPs in a population? How to find significant SNP variation between generations?
I have a population in the hundreds and did an Illumina pool-seq (ended up with ~100bp reads for the whole population).
I have the reference genome for the species and now need to align all the ...
- 249
1
vote
1
answer
66
views
Output of allelic association doesn't write the rsID [closed]
I'm using plink (1.9b5) to do allelic association. My problem is that my output does not write the rsID (SNP), it just writes a dot.
Output:
...
- 11
0
votes
0
answers
41
views
Is SNPRelate the goto package for PCA of SNP data in R?
I'm trying to evaluate a method that I'm not familiar with. They used SNPRelate. I'm wondering if this is the best / only choice... what other tools would you recommend?
Many thanks,
- 480
0
votes
1
answer
255
views
How to know the number of SNP in my samples after running the population module in stacks
I am new to stacks for analyzing RAD-Seq data, I have run all the modules. I will like to know to get the total SNP from my sample after running the population module. Is there a command line to use ...
- 19
0
votes
1
answer
146
views
Supplementary aligments in VAF
This question has also been asked on Biostars
I have a doubt, are supplementary alignment usually considered when the variant allele frequency is calculated? Thanks a lot.
In my case I have some ...
1
vote
0
answers
29
views
How to assess how prone genes may be to acquire structural polymorphisms?
I have 5 strains of P.falciparum. Each FASTA file has all its annotated CDSs. After a first pre-processing phase, where I eliminated the strangest sequences (perhaps the longest or shorter ones, which ...
- 147
1
vote
2
answers
92
views
RAD Seq Data Analysis without barcode
I received a ddRAD Seq data from my supervisor without barcodes and restriction enzymes. I asked him for both and he said I don't need it since the data has been cleaned by the company. Now, I am ...
- 19
1
vote
1
answer
79
views
Apply trained PRS on another dataset
I am using PRSice to compute the PRS over a train set and want to use the coefficient used on the train set to apply it on another set which I will call the test set.
Once I compute the PRS I get a ...
- 113
0
votes
1
answer
180
views
e-utils api: get chromosome position for each snp on a gene
So I have the following e-utils api-link:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=5726&retmode=json
it returns all the SNP-ids for the gene with ...
0
votes
1
answer
646
views
How can I extract all known mutations of my BAM (or SNP/INDL files)?
I am using a Genome Explorer tool to see all the mutations on my own DNA.
My particular interest is on listing the variants and get their names/ids.
Here are a few screenshots:
You can see that ...
- 143
1
vote
1
answer
391
views
How to calculate Centimorgan lengths from run lengths in one-to-one dna profile comparison
For easier management of a database of dna profiles, I'm creating a tool to perform one-to-one matching on two profiles with snp genotype information.
Basically, something that works similar to ...
- 113
5
votes
2
answers
3k
views
What does PCA mean on GWAS
I understand what GWAS is and I'm able to perform certain tests with the p-values, etc. But what I am having a hard time wrapping my head around is what PCA on GWAS means.
So let's say I have 100,000 ...
- 341
1
vote
1
answer
137
views
ncbi...eutils/esearch.fcgi: How to search now in the snp database?
According to the 2017(!) textbook, it worked at that time, for instance,
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=autism
At ...
- 113
5
votes
1
answer
1k
views
Does the ".full.aln" file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?
I have a number of sequences and a reference genome.
I used snippy to align each individual sequence with the reference genome. I then used ...
- 51
4
votes
1
answer
103
views
Statistical approach to compare the SNP genotyping data among set of individuals
So, I have the genotyping data of about 650,000 SNPs for 96 individuals. I already know the Y DNA haplogroup of these individuals, so to some extent, I have a gross understanding of their ancestry.
...
- 61
2
votes
1
answer
603
views
Can I export the SNPs between whole genome alignments using the command line?
I am using Mauve to align two whole genomes. I use the following command to get the alignment in xmfa format:
...
- 2,479
2
votes
1
answer
95
views
How to retrieve SNPs data of different humans?
How can I retrieve only SNPs from the dbSNP's FTP site. The files are gzipped and organized by human chromosome (i.e, chr[1-22,X,Y]), are these for one human? I need only SNPs data for various humans.
- 31
3
votes
2
answers
229
views
Is there a tool that can take a protein's amino acid sequence and would display it's locus on the genome?
I have the UNIPROT IDs, PDB IDs and FASTA files of several known proteins. I am looking for a tool that can take as input the protein's amino acid sequence and display the coding nucleotides of those ...
- 357
1
vote
1
answer
599
views
Where can I find a list of SNP rs IDs that belong to the X chromosome?
Where can I find a list of SNP rs IDs that belong to the X chromosome?
I'm trying to exclude the SNPs on X-chromosome in a data set, but I don't know where these SNPs come from.
I tried to use ...
- 521
6
votes
3
answers
247
views
Show presence of known mutation in RNA-seq data
We have RNA-seq fastq data from control (WT) patients and a patient with a point mutation at a known location in one gene.
I'd like to retrieve the reads aligning to that gene and show the presence of ...
- 2,644
6
votes
4
answers
4k
views
Convert rs ID of one hg build to rs IDs of another build
I have a list of dbSNP rsIDs for GRCh37 and I want to convert them to the equivalent IDs in GRCh38. This is using the most recent dbSNP build (150 as of the time of this post). Is there any ID mapping ...
- 221
7
votes
3
answers
154
views
How does one construct a cladogram of intraspecies relationships?
I have SNP data from several cultivars of rice which I have used to produce alignments, but I don't think that the usual models and algorithms used for generating phylogenetic trees are appropriate, ...
- 123